The decision to resume operations followed an emergency meeting at the airport, weighed up weather conditions, tests and data from AirNav and other groups, AirNav added.

Singapore Airlines said it would resume flights between Singapore and Bali on Wednesday. Qantas said it and budget arm Jetstar would run 16 flights to Australia on Thursday to ferry home 3,800 stranded customers.

A large plume of white and grey ash and smoke hovered above Agung on Wednesday, after night-time rain partially obscured a fiery glow at its peak over the last few days.

President Joko Widodo implored residents living in a zone around Agung deemed at risk to seek refuge in emergency centres, as winds sending an ash cloud southwest across the island once again halted flights.

A spokesman for Bali's I Gusti Ngurah Rai International Airport said as many as 430 domestic and international flights had been disrupted on Wednesday by the closure of the airport, about 60km away from Mt Agung.

The grounding of flights coincided with schoolies week in Australia, when an estimated 6000 teens were expected to flock to the island resort.

Mt Agung towers over eastern Bali to a height of just over 3,000 metres. Its last major eruption in 1963 killed more than 1,000 people and razed several villages.

Layers of ash coated cars, roofs and roads in an area southeast of the crater. Children wore masks to walk to school.

Authorities want residents in a radius of about 8km to 10km around the volcano to head for emergency centres, warning a larger eruption could be "imminent". But some are reluctant to leave homes and livestock unattended.